try to copy one box of smoke and paste in the new scene, I hope that the texture still there. Algodoo will probably associate this texture with the new scene. Also check the names of the textures. When you paste te box with the texture, compare its name on Appearence or Scripting with the Smoke Spawner's script. Note that if you resize it, you'll need a new textureMatrix.
I'd like to test it right now but I'll be able to access algodoo only in 5 hours
Hahaha, I already did that, but I didn't upload it. I recently made a scene with a thruster and another fire/smoke (untextured): http://www.algodoo.com/algobox/details.php?id=77294